EPIC-XS consortium members who attended the kick-off meeting in Amsterdam, from left to right: Javier Munoz, Centro Nacional de Investigaciones Oncologicas, Madrid, Spain; Marteen Altelaar, Utrecht University, The Netherlands; Tiziana Bonaldi, Inistituto Europeo di Oncologia, Milan, Italy, and Kris Gevaert, Vlaams Instituut voor Biotechnologie, Ghent.
The European Proteomics Infrastructure Consortium providing access (EPIC-XS), funded as part of the Horizon 2020 Work programme, held its kick-off meeting in Amsterdam on April 25-26 2019. This meeting brought together a consortium of world-leading European proteomics experts with the shared goal of supporting excellent life sciences research in Europe. Representatives from all eighteen* participating member countries, from young scientists to proteomics experts, had the opportunity to meet one another in a relaxed and informal setting and discuss important issues related to European guidelines.
“The kick-off meeting in Amsterdam was absolutely terrific from the perspective of a young scientist. On one hand, it solved administrative questions regarding public access to the best proteomic facilities across Europe, whilst also giving a great impression of the local research activities at the different partner sites. Now, I am eagerly waiting for the first access project to arrive at our site.” – Florian Bayer, Postdoctoral student, Technical University of Munich, Germany.
Paving the way for scientific advancements, however, can prove challenging. Luckily, some of these challenges had previously been addressed in the European funded proteomics imitative, PRIME-XS, which finished in 2011 after running for four years. This initiative was successful in its efforts of bringing the proteomics community together as a more coordinated scientific proteomic effort. Unfortunately, its sustainability was short-lived, and it had not sufficiently dealt with the issue of establishing a more internationally unified proteomics platform.
To this end, the EPIC-XS consortium is already on a winning formula, as the community has expanded its consortium to include seven new European partners. Hence, transnational access for all life science researchers to state of the art proteomics facilities has also been extended from six sites in PRIME-XS to eleven sites in EPIC-XS, providing approximately 2400 days accessibility to top of the range proteomics technology and access to its unparalleled expertise.
The kick-off meeting began with a brief introduction from Professor Albert Heck, project coordinator, and professor of biomolecular mass spectrometry and proteomics at Utrecht University, who explained the origin of the project, from its inception in 2017, to the kick-off and the project’s completion in December 2022. The essence of his talk embodied the determination of all members to provide and meet current demands for access to world-leading facilities and expertise, and in doing so to open up entirely new perspectives in proteomics.
While funding may have run its course by the end of 2022, the sustainability of the proteomics community, through this initiative, will continue to strengthen and develop long into the future. That this goal is achievable could be felt by the infectious enthusiasm of the consortium members who proudly presented state of the art technologies and expertise available at their institutions.
While this project is to be highly commended, like most ambitious projects it’s not without its challenges. The difference here, however, is that many lessons can be, and have been learnt from PRIME-XS as Reinout Raijmakers, (team leader, research support office, Utrecht University), explained. The importance of carrying out pilot studies cannot be over emphasized, saving valuable time and effort and ensuring that applicants’ expectations are realistic. That open access is key, was a point reinforced by Professor Kris Gevaert from the Vlaams Instituut voor Biotechnologie (VIB, Ghent) in his presentation, not only with respect to trans-national access, where submissions are permitted nationally, as well as internationally, but also with respect to ensuring all publications are freely available online.
Open access to data was also addressed by the ELIXIR ESFRI community. This bioinformatic proteomics consortium, led by EPIC-XS partners professor Juan Antonio Vizcaino (proteomics Team Leader at the EMBL-European Bioinformatics Institute, UK) Professor Oliver Kohlbacher (Eberhard Karl’s University Tübingen, Germany), Professor Lennart Martens (VIB, Ghent) and had met the day before the kick-off, to discuss “Proteomic Privacy: Re-identification Risk in Clinical Proteomics Data and Implications for Proteomics Data Management.”
The meeting constituted a first step to openly discuss and document privacy issues related to clinical proteomics data, a well-known topic for researchers working with DNA/RNA sequencing data. However, only very recently, analogous concerns have started to arise in the proteomics field. Some of these are related to the recent enforcement of the European Union General Data Protection Regulation guidelines, documented in May 2018. With increasing proteome coverage, searches against personalized proteome databases and error-tolerant database searches, variants can indeed be routinely be identified on the proteome level. Other data types also have the potential to be patient-identifiable, such as post-translational modification (PTM) profiles and protein expression levels. As a consequence, the current policies of full open data sharing in the US and in Europe may need to be revised.
The ambitiousness of this project in overcoming challenges was once again reflected in the impressive cutting-edge Joint Research Activities (JRA’s) presented on day two. The four JRA’s:
- “Computational Proteomics and Cross–Omics Integration,” presented by Professor Lennart Martens, (VIB, Ghent)
- “Future and Emerging Proteomics Technologies,” presented by Professor Julia Chamot-Rooke, (Institute Pasteur, France)
- “Translational Proteomics” presented by associate Professor Maarten Altelaar, (Utrecht University) and
- “Proteome Organization – Structural and Spatial Proteomics,” presented by Professor Alexander Leitner, (ETH, Swiss Federal Institute of Technology Zurich)
are built on the extremely strong innovative track-record of the consortium members involved and are focused on designing novel approaches for future developmental efforts in computational and structural proteomics as well as addressing the more challenging topics including single cell proteomics, cross-linking mass spectrometry, higher order proteome organization, multi-omics integration, native proteomics, translational/clinical proteomics and personalized/precision medicine. These JRA’s will also tackle logistical hurdles arising from the plethora of datasets that can be generated by proteomics methodologies.
“It was great to become acquainted with the EPIC-XS community, with so much expertise we look forward to contributing to significant advancements in proteomics research,” – Charlotte Stadler, PhD, SciLifelab, Stockholm, Sweden.
The proteomics community will also benefit from expertise in the field via training courses and workshops. The first of these workshops, organized together with FEBS on Chromatin Proteomics, will take place in Greece in September this year. Further information can be found here.
The EPIC-XS consortium members can be proud that they are associated with such a concerted European effort, and if the kick-off meeting is an indication of the commitment by its proteomics experts, then global life science research has a very bright and sustainable future.
Submissions and further information can be found here.
“The kick-off meeting for the European Proteomics Infrastructure Consortium providing access (EPIC-XS) brought together the best European proteomics laboratories and researchers. There was a very positive atmosphere and a feeling of a shared commitment to bring state-of-the-art proteomics to the European research community. What I particularly liked was the focus on joint research activities with the clear objective to develop best practices and protocols for implementation across the Access Sites that are providing transnational access to all researchers within the EU and associated countries.” – Professor Jesper Olsen, University of Copenhagen, Denmark.
*Consortium members: Institut Pasteur, France (IP); Royal Institute of Technology, Sweden (KTH), Foundation of Research and Technology Hellas, Greece (FORTH); ETH Zurich (ETH/FGCZ); Technical University of Munich, Germany (TUM); University of Bergen, Norway (UIB); University of Tartu, Estonia (UT); University of Copenhagen, Denmark (UCPH); Flemish Institute for Biotechnology, Ghent (VIB); European Bioinformatics Institute, UK (EBI); Research Institute of Molecular Pathology, Austria (IMP); Utrecht University (UU); European Institute of Oncology, Italy (IEO); Institute of Microbiology, Czech Republic (IMIC/CEITEC); University of Cambridge, UK (UCAM); Spanish National Cancer Research Centre (CNIO); Centre for Genomic Regulation (Spain) (CRG); Eberhard Karl’s University Tübingen, Germany (EKUT).